The deep biosphere—a realm of sediments buried far below the seafloor—harbors diverse, thriving communities of life, according a new study by scientists at Woods Hole Oceanographic Institution (WHOI) and the University of Delaware (UD).

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The researchers analyzed messenger RNA (mRNA) from 16 to 522 feet deep below the seafloor off the coast of Peru in 2002. They found evidence of bacteria, archaea, and fungi actively metabolizing, proliferating, and moving. Their work was published June 12, 2013, in Nature.

This first glimpse into the workings of the heretofore hidden ecosystem was made possible by the first successful extraction of total mRNA, or the "metatranscriptome," from the deep biosphere, said WHOI postdoctoral investigator Bill Orsi, who was lead author of the study.

Messenger RNA is highly sought after by microbial ecologists because its presence indicates that the cells that made it are still alive, and because it carries the instructions for cells to manufacture proteins. That gives researchers valuable information about the biochemical processes the organisms are using to function.

According to Orsi, extracting enough mRNA to conduct the studies was a difficult task because metabolic rates of microorganisms in the deep biosphere are very low and mRNA is only about 4 to 10 percent of the total RNA they make. "There’s a certain amount of banging your head against the wall before it works," he said.

Among the proteins they found coded for in the mRNA, many are involved in cell division, indicating that the cells that made them belong to growing populations.

The scientists also identified mRNAs for specific biochemical processes that use sulfates and nitrates, revealing new insights into the workings of the deep biosphere ecosystem. Particularly surprising was the discovery that fungi were metabolically active players contributing to the subseafloor ecosystem, along with bacteria and archaea.

The researchers also found evidence that cells in the deep biosphere are eating amino acids, which are a rich source of carbon and nitrogen and can only have come from other living or recently deceased organisms. The scientists think those amino acids came from cells that lived and died in the deep biosphere, rather than remnants that drifted down through the water.